I imagine they'll play a secondary role in the main plot. Well all be fighting to restore humanity, but these factions might also be vying for governmental control over the new age of mankind.
There may be small missions against the other factions... Stealing intel, supplies, things like that. Probably not all out war. (Except for the competative multiplayer experience, "faction wars").

Well a quick googling of Seraphim turns up this:
"Medieval Christian theology places seraphs in the highest choir of the angelic hierarchy. They are the caretakers of God's throne, continuously singing "holy, holy, holy"."
-Wikipedia
So, we could take that to mean that they consider themselves the caretakers of the Traveler. Also, I think that they may be the air superiority due to Seraphim being angels, which, hopefully you all know come from Heaven(or the heavens[space]).